X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=194b18fa7353f44e7756016f0e8c1f303416052b;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=2fca07de2545fd692a778611af55eb5f287b502f;hpb=52402128d98c6744eb6348dd788fe6e8cd34575c;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 2fca07d..194b18f 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -27,7 +27,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.io.FeaturesFile; import jalview.schemes.FeatureColour; -import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -36,7 +36,9 @@ import java.awt.Button; import java.awt.Choice; import java.awt.Color; import java.awt.Dimension; +import java.awt.FlowLayout; import java.awt.Font; +import java.awt.Frame; import java.awt.Graphics; import java.awt.GridLayout; import java.awt.Label; @@ -48,7 +50,10 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import java.awt.event.TextEvent; +import java.awt.event.TextListener; import java.util.Hashtable; +import java.util.List; /** * DOCUMENT ME! @@ -56,9 +61,16 @@ import java.util.Hashtable; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer extends - jalview.renderer.seqfeatures.FeatureRenderer +public class FeatureRenderer + extends jalview.renderer.seqfeatures.FeatureRenderer { + /* + * creating a new feature defaults to the type and group as + * the last one created + */ + static String lastFeatureAdded = "feature_1"; + + static String lastFeatureGroupAdded = "Jalview"; // Holds web links for feature groups and feature types // in the form label|link @@ -75,12 +87,6 @@ public class FeatureRenderer extends } - static String lastFeatureAdded; - - static String lastFeatureGroupAdded; - - static String lastDescriptionAdded; - int featureIndex = 0; boolean deleteFeature = false; @@ -165,13 +171,25 @@ public class FeatureRenderer extends } - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean newFeatures, + /** + * Shows a dialog allowing the user to create, or amend or delete, sequence + * features. If null in the supplied feature(s), feature type and group + * default to those for the last feature created (with initial defaults of + * "feature_1" and "Jalview"). + * + * @param sequences + * @param features + * @param create + * @param ap + * @return + */ + boolean amendFeatures(final List sequences, + final List features, boolean create, final AlignmentPanel ap) { - Panel bigPanel = new Panel(new BorderLayout()); + final Panel bigPanel = new Panel(new BorderLayout()); final TextField name = new TextField(16); - final TextField source = new TextField(16); + final TextField group = new TextField(16); final TextArea description = new TextArea(3, 35); final TextField start = new TextField(8); final TextField end = new TextField(8); @@ -179,6 +197,22 @@ public class FeatureRenderer extends Button deleteButton = new Button("Delete"); deleteFeature = false; + name.addTextListener(new TextListener() + { + @Override + public void textValueChanged(TextEvent e) + { + warnIfTypeHidden(ap.alignFrame, name.getText()); + } + }); + group.addTextListener(new TextListener() + { + @Override + public void textValueChanged(TextEvent e) + { + warnIfGroupHidden(ap.alignFrame, group.getText()); + } + }); colourPanel = new FeatureColourPanel(); colourPanel.setSize(110, 15); final FeatureRenderer fr = this; @@ -190,22 +224,20 @@ public class FeatureRenderer extends // ///////////////////////////////////// // /MULTIPLE FEATURES AT SELECTED RESIDUE - if (!newFeatures && features.length > 1) + if (!create && features.size() > 1) { panel = new Panel(new GridLayout(4, 1)); tmp = new Panel(); tmp.add(new Label("Select Feature: ")); overlaps = new Choice(); - for (int i = 0; i < features.length; i++) + for (SequenceFeature sf : features) { - String item = features[i].getType() + "/" + features[i].getBegin() - + "-" + features[i].getEnd(); - - if (features[i].getFeatureGroup() != null) + String item = sf.getType() + "/" + sf.getBegin() + "-" + + sf.getEnd(); + if (sf.getFeatureGroup() != null) { - item += " (" + features[i].getFeatureGroup() + ")"; + item += " (" + sf.getFeatureGroup() + ")"; } - overlaps.addItem(item); } @@ -220,15 +252,16 @@ public class FeatureRenderer extends if (index != -1) { featureIndex = index; - name.setText(features[index].getType()); - description.setText(features[index].getDescription()); - source.setText(features[index].getFeatureGroup()); - start.setText(features[index].getBegin() + ""); - end.setText(features[index].getEnd() + ""); + SequenceFeature sf = features.get(index); + name.setText(sf.getType()); + description.setText(sf.getDescription()); + group.setText(sf.getFeatureGroup()); + start.setText(sf.getBegin() + ""); + end.setText(sf.getEnd() + ""); SearchResultsI highlight = new SearchResults(); - highlight.addResult(sequences[0], features[index].getBegin(), - features[index].getEnd()); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); ap.seqPanel.seqCanvas.highlightSearchResults(highlight); @@ -236,7 +269,7 @@ public class FeatureRenderer extends FeatureColourI col = getFeatureStyle(name.getText()); if (col == null) { - Color generatedColour = UserColourScheme + Color generatedColour = ColorUtils .createColourFromName(name.getText()); col = new FeatureColour(generatedColour); } @@ -252,17 +285,20 @@ public class FeatureRenderer extends tmp = new Panel(); panel.add(tmp); - tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.name:"), + Label.RIGHT)); tmp.add(name); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT)); - tmp.add(source); + tmp.add(new Label(MessageManager.getString("label.group:"), + Label.RIGHT)); + tmp.add(group); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.colour"), + Label.RIGHT)); tmp.add(colourPanel); bigPanel.add(panel, BorderLayout.NORTH); @@ -272,7 +308,7 @@ public class FeatureRenderer extends Label.RIGHT)); panel.add(new ScrollPane().add(description)); - if (!newFeatures) + if (!create) { bigPanel.add(panel, BorderLayout.SOUTH); @@ -290,46 +326,33 @@ public class FeatureRenderer extends bigPanel.add(panel, BorderLayout.CENTER); } - if (lastFeatureAdded == null) - { - if (features[0].type != null) - { - lastFeatureAdded = features[0].type; - } - else - { - lastFeatureAdded = "feature_1"; - } - } - - if (lastFeatureGroupAdded == null) - { - if (features[0].featureGroup != null) - { - lastFeatureGroupAdded = features[0].featureGroup; - } - else - { - lastFeatureAdded = "Jalview"; - } - } - - String title = newFeatures ? MessageManager - .getString("label.create_new_sequence_features") + /* + * use defaults for type and group (and update them on Confirm) only + * if feature type has not been supplied by the caller + * (e.g. for Amend, or create features from Find) + */ + SequenceFeature firstFeature = features.get(0); + boolean useLastDefaults = firstFeature.getType() == null; + String featureType = useLastDefaults ? lastFeatureAdded + : firstFeature.getType(); + String featureGroup = useLastDefaults ? lastFeatureGroupAdded + : firstFeature.getFeatureGroup(); + + String title = create + ? MessageManager.getString("label.create_new_sequence_features") : MessageManager.formatMessage("label.amend_delete_features", - new String[] { sequences[0].getName() }); + new String[] + { sequences.get(0).getName() }); final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385, 240); dialog.setMainPanel(bigPanel); - if (newFeatures) - { - name.setText(lastFeatureAdded); - source.setText(lastFeatureGroupAdded); - } - else + name.setText(featureType); + group.setText(featureGroup); + + if (!create) { dialog.ok.setLabel(MessageManager.getString("label.amend")); dialog.buttonPanel.add(deleteButton, 1); @@ -342,13 +365,11 @@ public class FeatureRenderer extends dialog.setVisible(false); } }); - name.setText(features[0].getType()); - source.setText(features[0].getFeatureGroup()); } - start.setText(features[0].getBegin() + ""); - end.setText(features[0].getEnd() + ""); - description.setText(features[0].getDescription()); + start.setText(firstFeature.getBegin() + ""); + end.setText(firstFeature.getEnd() + ""); + description.setText(firstFeature.getDescription()); // lookup (or generate) the feature colour FeatureColourI fcol = getFeatureStyle(name.getText()); // simply display the feature color in a box @@ -375,34 +396,33 @@ public class FeatureRenderer extends FeaturesFile ffile = new FeaturesFile(); - if (dialog.accept) - { - // This ensures that the last sequence - // is refreshed and new features are rendered - lastSeq = null; - lastFeatureAdded = name.getText().trim(); - lastFeatureGroupAdded = source.getText().trim(); - lastDescriptionAdded = description.getText().replace('\n', ' '); - } - - if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1) + /* + * only update default type and group if we used defaults + */ + String enteredType = name.getText().trim(); + if (dialog.accept && useLastDefaults) { - lastFeatureGroupAdded = null; + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = group.getText().trim(); } - if (!newFeatures) + if (!create) { - - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features.get(featureIndex); if (dialog.accept) { - sf.type = lastFeatureAdded; - sf.featureGroup = lastFeatureGroupAdded; - sf.description = lastDescriptionAdded; + sf.type = enteredType; + sf.featureGroup = group.getText().trim(); + if (sf.featureGroup != null && sf.featureGroup.length() < 1) + { + sf.featureGroup = null; + } + sf.description = description.getText().replace('\n', ' '); if (!colourPanel.isGcol) { // update colour - otherwise its already done. - setColour(sf.type, new FeatureColour(colourPanel.getBackground())); + setColour(sf.type, + new FeatureColour(colourPanel.getBackground())); } try { @@ -410,42 +430,46 @@ public class FeatureRenderer extends sf.end = Integer.parseInt(end.getText()); } catch (NumberFormatException ex) { + // } + boolean typeOrGroupChanged = (!featureType.equals(sf.type) + || !featureGroup.equals(sf.featureGroup)); ffile.parseDescriptionHTML(sf, false); - setVisible(lastFeatureAdded); // if user edited name then make sure new - // type is visible + if (typeOrGroupChanged) + { + featuresAdded(); + } } if (deleteFeature) { - sequences[0].deleteFeature(sf); + sequences.get(0).deleteFeature(sf); + // ensure Feature Settings reflects removal of feature / group + featuresAdded(); } - } else { + /* + * adding feature(s) + */ if (dialog.accept && name.getText().length() > 0) { - for (int i = 0; i < sequences.length; i++) + for (int i = 0; i < sequences.size(); i++) { - features[i].type = lastFeatureAdded; - features[i].featureGroup = lastFeatureGroupAdded; - features[i].description = lastDescriptionAdded; - sequences[i].addSequenceFeature(features[i]); - ffile.parseDescriptionHTML(features[i], false); + features.get(i).type = enteredType; + features.get(i).featureGroup = group.getText().trim(); + features.get(i).description = description.getText().replace('\n', + ' '); + sequences.get(i).addSequenceFeature(features.get(i)); + ffile.parseDescriptionHTML(features.get(i), false); } Color newColour = colourPanel.getBackground(); // setColour(lastFeatureAdded, fcol); - if (lastFeatureGroupAdded != null) - { - setGroupVisibility(lastFeatureGroupAdded, true); - } - setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol - setVisible(lastFeatureAdded); - findAllFeatures(false); // different to original applet behaviour ? - // findAllFeatures(); + setColour(enteredType, new FeatureColour(newColour)); // was fcol + featuresAdded(); } else { @@ -464,4 +488,43 @@ public class FeatureRenderer extends return true; } + + protected void warnIfGroupHidden(Frame frame, String group) + { + if (featureGroups.containsKey(group) && !featureGroups.get(group)) + { + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.group"), group); + showWarning(frame, msg); + } + } + + protected void warnIfTypeHidden(Frame frame, String type) + { + if (getRenderOrder().contains(type)) + { + if (!showFeatureOfType(type)) + { + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.feature_type"), type); + showWarning(frame, msg); + } + } + } + + /** + * @param frame + * @param msg + */ + protected void showWarning(Frame frame, String msg) + { + JVDialog d = new JVDialog(frame, "", true, 350, 200); + Panel mp = new Panel(); + d.ok.setLabel(MessageManager.getString("action.ok")); + d.cancel.setVisible(false); + mp.setLayout(new FlowLayout()); + mp.add(new Label(msg)); + d.setMainPanel(mp); + d.setVisible(true); + } }